Difference between revisions of "Team:NTNU Trondheim/Experiments"

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<div class="column full_size">
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<head>
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    <link href="https://fonts.googleapis.com/icon?family=Material+Icons" rel="stylesheet">
  
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<h1>Lab Journal</h1>
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    <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/materialize/1.0.0-rc.2/css/materialize.min.css">
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<p>Describe the research, experiments, and protocols you used in your iGEM project. These should be detailed enough for another team to repeat your experiments.</p>
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<p>
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    <script src="https://cdnjs.cloudflare.com/ajax/libs/materialize/1.0.0-rc.2/js/materialize.min.js"></script>
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Please remember to put all characterization and measurement data for your parts on the corresponding Registry part pages.  
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</p>
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<h1>Lab Journal<br></h1>
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<h3>What should this page contain?</h3>
+
<p><br></p>
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<ul>
+
 
−
<li> Protocols </li>
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  <!------------------------------------------- WHOLE NOTEBOOK --------------------------------------------->
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<li> Experiments </li>
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  <ul class="collapsible">
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<li> Documentation of the development of your project </li>
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            <p style="font-size:110%;"><b>NOTE TITLE</b></p></div>
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                    Test.
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            <p><b>Note title</b></p></div>
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            <div class="collapsible-body"><span>Lorem ipsum dolor sit amet.</span></div>
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            <p><b>Our first day in the laboratory!</b></p></div>
 +
            <div class="collapsible-body"><span> <b>Goal:</b> Incubate the Escherichia coli (E. coli) samples which carry pgRNA and pdCas9 on agar plates with antibiotics.<br>
 +
<br>
 +
<b> Preparation of LA- medium </b>
 +
<br>
 +
LA- medium (1.5%) were made after the following recipe, and autoclaved for 20min at 121°C.
 +
 
 +
<ul>
 +
<li> 1L      Distilled water </li>
 +
 
 +
<li>5g        Yeast extract </li>
 +
 
 +
<li>10g      Tryptone </li>
 +
 
 +
<li>5g        NaCl</li>
 +
 
 +
<li>15g      Agar </li>
 
</ul>
 
</ul>
 +
<br>
  
−
</div>
+
<b>Agar plates with antibiotics </b> <br>
 +
 
 +
Two different agar plates were made – one type contains ampicillin (AMP) while the other type contains chloramphenicol (CM), and were prepared after the following recipe:
 +
<br>
 +
<br>
 +
LA- medium with AMP:
  
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<div class="column third_size">
 
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<div class="highlight decoration_A_full">
 
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<h3>Inspiration</h3>
 
 
<ul>
 
<ul>
−
<li><a href="https://2014.igem.org/Team:Colombia/Protocols">2014 Colombia </a></li>
+
 
−
<li><a href="https://2014.igem.org/Team:Imperial/Protocols">2014 Imperial </a></li>
+
<li>0.5L    LA-medium </li>
−
<li><a href="https://2014.igem.org/Team:Caltech/Project/Experiments">2014 Caltech </a></li>
+
 
 +
<li>0.5mL AMP (50mg/mL)</li>
 
</ul>
 
</ul>
−
</div>
+
 
−
</div>
+
LA-medium with CM:
 +
<ul>
 +
<li>0.5L    LA-medium</li>
 +
 
 +
<li>0.5mL CM (35mg/mL)</li>
 +
</ul>
 +
 
 +
<br>
 +
The LA-media with antibiotic were poured on petri dishes.
 +
<br>
 +
<br>
 +
<b>Incubation of bacteria </b>
 +
<br>
 +
 
 +
Two Escherichia coli (E. coli) samples which carry pgRNA and pdCas9 plasmids respectively, were ordered from Addgene. E.coli which carry the pgRNA plasmid were plated on agar plates with AMP, while E.coli which carry the pdCas9 plasmid were plated on two agar plates with CM, and incubated at 37℃.
 +
<br>
 +
<br>
 +
<b>Results: </b>
 +
<br>
 +
The E.coli with pgRNA and pdCas9 formed colonies on the agar plates with AMP and CM
 +
 
 +
</span></div>
 +
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              </div>
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 +
            <p><b>Inoculation of E.coli</b></p></div>
 +
            <div class="collapsible-body"><span>
 +
<b>Goal:</b> Inoculate a colony from each agar plate which were prepared from the previous day, in LB- medium with antibiotics. <br>
 +
<br>
 +
<b>Procedure</b> <br>
 +
One colony of pgRNA- and pdCas9- bacteria grown overnight on agar plates were picked and inoculated in LB-media (25mL) with AMP (25μL) and CM (25μL), respectively. The cell cultures were incubated at 37℃ in a shaking incubator at 204rpm. <br>
 +
</span></div>
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                  Jun
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                  22
 +
                </div>
 +
              </div>
 +
            </div>
 +
            <p><b>Isolation and verification of pgRNA and pdCas9</b></p></div>
 +
            <div class="collapsible-body"><span>
 +
<b>Goal:</b> Isolate and verify that the E.coli carry pgRNA and pdCas9.<br>
 +
<br>
 +
<b>Plasmid isolation</b><br>
 +
pgRNA and pdCas9 were isolated from the incubated bacteria prepared yesterday (June 21) by following the protocol of <font color="#0000e6">ZR Plasmid Miniprep Kit</font>:<br>
 +
<ol>
 +
  <li>1mL of each cell culture (which either carry pgRNA or pdCas9) were transferred to eppendorf tube and centrifugated for 20s at 16000g</li>
 +
  <li>The supernatant was discarded, while the pellet was resuspended in buffer</li>
 +
  <li>Lysing buffer was added to the sample and carefully mixed in 2min</li>
 +
  <li>Neutralizing buffer was added to the sample, and mixed until the colour of the solution became yellow</li>
 +
  <li>The solution was centrifugated for 2min at 16000g</li>
 +
  <li>The supernatant was collected and transferred to column in a collection tube, and centrifugated for 30s at 16000g</li>
 +
  <li>The supernatant in the collection tube was discarded</li>
 +
  <li>Endo-wash buffer was added to the column and centrifugated for 1min at 16000g</li>
 +
  <li>Plasmid- wash buffer was added to the column and centrifugated for 1 min at 16000g</li>
 +
  <li>The solution in the collection tube was discarded, while the column with plasmids was transferred to a new collection tube</li>
 +
  <li>The plasmids in the column were eluted by adding 30μL distilled water, and centrifugated for 30s in 16000g</li>
 +
</ol>
 +
<br>
 +
<b>Determine plasmid concentration and purity</b><br>
 +
The concentration of plasmids and the purity of each sample were determined by using Nanodrop.<br>
 +
<br>
 +
<b>Restriction digest and plasmid verification</b><br>
 +
The presence of pgRNA and pdCas9 in the cell cultures were verified after following the restriction digest protocol and separation of the DNA fragments by gel electrophoresis.
 +
 
 +
 
 +
</span></div>
 +
          </li>
 +
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            <p>Note title</p></div>
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            <p>Note title</p></div>
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            <div class="collapsible-body"><span>Lorem ipsum dolor sit amet.</span></div>
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                  Jun
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                  26
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              </div>
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            </div>
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            <p>Note title</p></div>
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            <div class="collapsible-body"><span>Lorem ipsum dolor sit amet.</span></div>
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                  Jun
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            <p>Note title</p></div>
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            <div class="collapsible-body"><span>Lorem ipsum dolor sit amet.</span></div>
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                  Jun
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                  28
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            <p>Note title</p></div>
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            <div class="collapsible-body"><span>Lorem ipsum dolor sit amet.</span></div>
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                  Jun
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                  29
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              </div>
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            </div>
 +
            <p>Note title</p></div>
 +
            <div class="collapsible-body"><span>Lorem ipsum dolor sit amet.</span></div>
 +
          </li>
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        </ul>
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                  27
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              </div>
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            </div>
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            <p>Note title</p></div>
 +
      <div class="collapsible-body"><span>
 +
        <!----------------------------------------- DAYS IN WEEK ------------------------------------------->
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                  Jul
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                  1
 +
                </div>
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              </div>
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            </div>
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            <p>Note title</p></div>
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            <div class="collapsible-body"><span></span></div>
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                  Jul
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              </div>
 +
            </div>
 +
            <p>InterLabs Study</p></div>
 +
            <div class="collapsible-body"><span> Calibration 1 and 2 for the InterLabs Study.</span></div>
 +
          </li>
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                  Jul
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                  3
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              </div>
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            </div>
 +
            <p>Note title</p></div>
 +
            <div class="collapsible-body"><span>Lorem ipsum dolor sit amet.</span></div>
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          </li>
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              </div>
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            </div>
 +
            <p>Note title</p></div>
 +
            <div class="collapsible-body"><span>Lorem ipsum dolor sit amet.</span></div>
 +
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              </div>
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            </div>
 +
            <p>Note title</p></div>
 +
            <div class="collapsible-body"><span>Lorem ipsum dolor sit amet.</span></div>
 +
          </li>
 +
 
 +
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                </div>
 +
                <div class="date-display-day">
 +
                  28
 +
                </div>
 +
              </div>
 +
            </div>
 +
            <p>Note title</p></div>
 +
      <div class="collapsible-body"><span>
 +
 
 +
        <!----------------------------------------- DAYS IN WEEK ------------------------------------------->
 +
        <ul class="collapsible">
 +
          <li>
 +
            <div class="collapsible-header">
 +
              <div class="date-display">
 +
              <div class="date-display-cal">
 +
                <div class="date-display-month">
 +
                  Jul
 +
                </div>
 +
                <div class="date-display-day">
 +
                  9
 +
                </div>
 +
              </div>
 +
            </div>
 +
            <p>Note title</p></div>
 +
            <div class="collapsible-body"><span>Lorem ipsum dolor sit amet.</span></div>
 +
          </li>
 +
            <li>
 +
          <div class="collapsible-header">
 +
              <div class="date-display">
 +
              <div class="date-display-cal">
 +
                <div class="date-display-month">
 +
                  Jul
 +
                </div>
 +
                <div class="date-display-day">
 +
                  10
 +
                </div>
 +
              </div>
 +
            </div>
 +
            <p>Note title</p></div>
 +
            <div class="collapsible-body"><span>Lorem ipsum dolor sit amet.</span></div>
 +
          </li>
 +
            <li>
 +
          <div class="collapsible-header">
 +
              <div class="date-display">
 +
              <div class="date-display-cal">
 +
                <div class="date-display-month">
 +
                  Jul
 +
                </div>
 +
                <div class="date-display-day">
 +
                  11
 +
                </div>
 +
              </div>
 +
            </div>
 +
            <p>Note title</p></div>
 +
            <div class="collapsible-body"><span>Lorem ipsum dolor sit amet.</span></div>
 +
          </li>
 +
            <li>
 +
          <div class="collapsible-header">
 +
              <div class="date-display">
 +
              <div class="date-display-cal">
 +
                <div class="date-display-month">
 +
                  Jul
 +
                </div>
 +
                <div class="date-display-day">
 +
                  12
 +
                </div>
 +
              </div>
 +
            </div>
 +
            <p>Note title</p></div>
 +
            <div class="collapsible-body"><span>Lorem ipsum dolor sit amet.</span></div>
 +
          </li>
 +
            <li>
 +
          <div class="collapsible-header">
 +
              <div class="date-display">
 +
              <div class="date-display-cal">
 +
                <div class="date-display-month">
 +
                  Jul
 +
                </div>
 +
                <div class="date-display-day">
 +
                  13
 +
                </div>
 +
              </div>
 +
            </div>
 +
            <p>Note title</p></div>
 +
            <div class="collapsible-body"><span>Lorem ipsum dolor sit amet.</span></div>
 +
          </li>
 +
 
 +
        </ul>
 +
        <!-------------------------------------- END OF DAYS IN WEEK ---------------------------------------->
 +
 
 +
      </li>
 +
 
 +
        <!------------------------------------------- END OF WEEK --------------------------------------------->
 +
 
 +
 +
 
 +
<!------------------------------------------- WEEK --------------------------------------------------->
 +
      <li>
 +
      <div class="collapsible-header">
 +
          <div class="date-display">
 +
              <div class="date-display-cal">
 +
                <div class="date-display-month">
 +
                  Week
 +
                </div>
 +
                <div class="date-display-day">
 +
                  29
 +
                </div>
 +
              </div>
 +
            </div>
 +
            <p>Note title</p></div>
 +
      <div class="collapsible-body"><span>
 +
 
 +
        <!----------------------------------------- DAYS IN WEEK ------------------------------------------->
 +
        <ul class="collapsible">
 +
          <li>
 +
            <div class="collapsible-header">
 +
              <div class="date-display">
 +
              <div class="date-display-cal">
 +
                <div class="date-display-month">
 +
                  Jul
 +
                </div>
 +
                <div class="date-display-day">
 +
                  16
 +
                </div>
 +
              </div>
 +
            </div>
 +
            <p>Note title</p></div>
 +
            <div class="collapsible-body"><span>Lorem ipsum dolor sit amet.</span></div>
 +
          </li>
 +
            <li>
 +
          <div class="collapsible-header">
 +
              <div class="date-display">
 +
              <div class="date-display-cal">
 +
                <div class="date-display-month">
 +
                  Jul
 +
                </div>
 +
                <div class="date-display-day">
 +
                  17
 +
                </div>
 +
              </div>
 +
            </div>
 +
            <p>Note title</p></div>
 +
            <div class="collapsible-body"><span>Lorem ipsum dolor sit amet.</span></div>
 +
          </li>
 +
            <li>
 +
          <div class="collapsible-header">
 +
              <div class="date-display">
 +
              <div class="date-display-cal">
 +
                <div class="date-display-month">
 +
                  Jul
 +
                </div>
 +
                <div class="date-display-day">
 +
                  18
 +
                </div>
 +
              </div>
 +
            </div>
 +
            <p>Note title</p></div>
 +
            <div class="collapsible-body"><span>Lorem ipsum dolor sit amet.</span></div>
 +
          </li>
 +
            <li>
 +
          <div class="collapsible-header">
 +
              <div class="date-display">
 +
              <div class="date-display-cal">
 +
                <div class="date-display-month">
 +
                  Jul
 +
                </div>
 +
                <div class="date-display-day">
 +
                  19
 +
                </div>
 +
              </div>
 +
            </div>
 +
            <p>Note title</p></div>
 +
            <div class="collapsible-body"><span>Lorem ipsum dolor sit amet.</span></div>
 +
          </li>
 +
            <li>
 +
          <div class="collapsible-header">
 +
              <div class="date-display">
 +
              <div class="date-display-cal">
 +
                <div class="date-display-month">
 +
                  Jul
 +
                </div>
 +
                <div class="date-display-day">
 +
                  20
 +
                </div>
 +
              </div>
 +
            </div>
 +
            <p>Note title</p></div>
 +
            <div class="collapsible-body"><span>Lorem ipsum dolor sit amet.</span></div>
 +
          </li>
 +
 
 +
        </ul>
 +
        <!-------------------------------------- END OF DAYS IN WEEK ---------------------------------------->
 +
 
 +
      </li>
 +
 
 +
        <!------------------------------------------- END OF WEEK --------------------------------------------->
 +
<!------------------------------------------- WEEK --------------------------------------------------->
 +
      <li>
 +
      <div class="collapsible-header">
 +
          <div class="date-display">
 +
              <div class="date-display-cal">
 +
                <div class="date-display-month">
 +
                  Week
 +
                </div>
 +
                <div class="date-display-day">
 +
                  30
 +
                </div>
 +
              </div>
 +
            </div>
 +
            <p>Note title</p></div>
 +
      <div class="collapsible-body"><span>
 +
 
 +
        <!----------------------------------------- DAYS IN WEEK ------------------------------------------->
 +
        <ul class="collapsible">
 +
          <li>
 +
            <div class="collapsible-header">
 +
              <div class="date-display">
 +
              <div class="date-display-cal">
 +
                <div class="date-display-month">
 +
                  Jul
 +
                </div>
 +
                <div class="date-display-day">
 +
                  23
 +
                </div>
 +
              </div>
 +
            </div>
 +
            <p>Note title</p></div>
 +
            <div class="collapsible-body"><span>Lorem ipsum dolor sit amet.</span></div>
 +
          </li>
 +
            <li>
 +
          <div class="collapsible-header">
 +
              <div class="date-display">
 +
              <div class="date-display-cal">
 +
                <div class="date-display-month">
 +
                  Jul
 +
                </div>
 +
                <div class="date-display-day">
 +
                  24
 +
                </div>
 +
              </div>
 +
            </div>
 +
            <p>Note title</p></div>
 +
            <div class="collapsible-body"><span>Lorem ipsum dolor sit amet.</span></div>
 +
          </li>
 +
            <li>
 +
          <div class="collapsible-header">
 +
              <div class="date-display">
 +
              <div class="date-display-cal">
 +
                <div class="date-display-month">
 +
                  Jul
 +
                </div>
 +
                <div class="date-display-day">
 +
                  25
 +
                </div>
 +
              </div>
 +
            </div>
 +
            <p>Note title</p></div>
 +
            <div class="collapsible-body"><span>Lorem ipsum dolor sit amet.</span></div>
 +
          </li>
 +
            <li>
 +
          <div class="collapsible-header">
 +
              <div class="date-display">
 +
              <div class="date-display-cal">
 +
                <div class="date-display-month">
 +
                  Jul
 +
                </div>
 +
                <div class="date-display-day">
 +
                  26
 +
                </div>
 +
              </div>
 +
            </div>
 +
            <p>Note title</p></div>
 +
            <div class="collapsible-body"><span>Lorem ipsum dolor sit amet.</span></div>
 +
          </li>
 +
            <li>
 +
          <div class="collapsible-header">
 +
              <div class="date-display">
 +
              <div class="date-display-cal">
 +
                <div class="date-display-month">
 +
                  Jul
 +
                </div>
 +
                <div class="date-display-day">
 +
                  27
 +
                </div>
 +
              </div>
 +
            </div>
 +
            <p>Note title</p></div>
 +
            <div class="collapsible-body"><span>Lorem ipsum dolor sit amet.</span></div>
 +
          </li>
 +
 
 +
        </ul>
 +
        <!-------------------------------------- END OF DAYS IN WEEK ---------------------------------------->
 +
 
 +
      </li>
 +
 
 +
        <!------------------------------------------- END OF WEEK --------------------------------------------->
 +
<!------------------------------------------- WEEK --------------------------------------------------->
 +
      <li>
 +
      <div class="collapsible-header">
 +
          <div class="date-display">
 +
              <div class="date-display-cal">
 +
                <div class="date-display-month">
 +
                  Week
 +
                </div>
 +
                <div class="date-display-day">
 +
                  31
 +
                </div>
 +
              </div>
 +
            </div>
 +
            <p>Note title</p></div>
 +
      <div class="collapsible-body"><span>
 +
 
 +
        <!----------------------------------------- DAYS IN WEEK ------------------------------------------->
 +
        <ul class="collapsible">
 +
          <li>
 +
            <div class="collapsible-header">
 +
              <div class="date-display">
 +
              <div class="date-display-cal">
 +
                <div class="date-display-month">
 +
                  Jul
 +
                </div>
 +
                <div class="date-display-day">
 +
                  30
 +
                </div>
 +
              </div>
 +
            </div>
 +
            <p>Note title</p></div>
 +
            <div class="collapsible-body"><span>Lorem ipsum dolor sit amet.</span></div>
 +
          </li>
 +
            <li>
 +
          <div class="collapsible-header">
 +
              <div class="date-display">
 +
              <div class="date-display-cal">
 +
                <div class="date-display-month">
 +
                  Jul
 +
                </div>
 +
                <div class="date-display-day">
 +
                  31
 +
                </div>
 +
              </div>
 +
            </div>
 +
            <p>Note title</p></div>
 +
            <div class="collapsible-body"><span>Lorem ipsum dolor sit amet.</span></div>
 +
          </li>
 +
            <li>
 +
          <div class="collapsible-header">
 +
              <div class="date-display">
 +
              <div class="date-display-cal">
 +
                <div class="date-display-month">
 +
                  Aug
 +
                </div>
 +
                <div class="date-display-day">
 +
                  1
 +
                </div>
 +
              </div>
 +
            </div>
 +
            <p>Note title</p></div>
 +
            <div class="collapsible-body"><span>Lorem ipsum dolor sit amet.</span></div>
 +
          </li>
 +
            <li>
 +
          <div class="collapsible-header">
 +
              <div class="date-display">
 +
              <div class="date-display-cal">
 +
                <div class="date-display-month">
 +
                  Aug
 +
                </div>
 +
                <div class="date-display-day">
 +
                  2
 +
                </div>
 +
              </div>
 +
            </div>
 +
            <p>Note title</p></div>
 +
            <div class="collapsible-body"><span>Lorem ipsum dolor sit amet.</span></div>
 +
          </li>
 +
            <li>
 +
          <div class="collapsible-header">
 +
              <div class="date-display">
 +
              <div class="date-display-cal">
 +
                <div class="date-display-month">
 +
                  Aug
 +
                </div>
 +
                <div class="date-display-day">
 +
                  3
 +
                </div>
 +
              </div>
 +
            </div>
 +
            <p>Note title</p></div>
 +
            <div class="collapsible-body"><span>Lorem ipsum dolor sit amet.</span></div>
 +
          </li>
 +
 
 +
        </ul>
 +
        <!-------------------------------------- END OF DAYS IN WEEK ---------------------------------------->
 +
 
 +
      </li>
 +
 
 +
        <!------------------------------------------- END OF WEEK --------------------------------------------->
 +
<!------------------------------------------- WEEK --------------------------------------------------->
 +
      <li>
 +
      <div class="collapsible-header">
 +
          <div class="date-display">
 +
              <div class="date-display-cal">
 +
                <div class="date-display-month">
 +
                  Week
 +
                </div>
 +
                <div class="date-display-day">
 +
                  32
 +
                </div>
 +
              </div>
 +
            </div>
 +
            <p>Note title</p></div>
 +
      <div class="collapsible-body"><span>
 +
 
 +
        <!----------------------------------------- DAYS IN WEEK ------------------------------------------->
 +
        <ul class="collapsible">
 +
          <li>
 +
            <div class="collapsible-header">
 +
              <div class="date-display">
 +
              <div class="date-display-cal">
 +
                <div class="date-display-month">
 +
                  Aug
 +
                </div>
 +
                <div class="date-display-day">
 +
                  6
 +
                </div>
 +
              </div>
 +
            </div>
 +
            <p>Note title</p></div>
 +
            <div class="collapsible-body"><span>Lorem ipsum dolor sit amet.</span></div>
 +
          </li>
 +
            <li>
 +
          <div class="collapsible-header">
 +
              <div class="date-display">
 +
              <div class="date-display-cal">
 +
                <div class="date-display-month">
 +
                  Aug
 +
                </div>
 +
                <div class="date-display-day">
 +
                  7
 +
                </div>
 +
              </div>
 +
            </div>
 +
            <p>Note title</p></div>
 +
            <div class="collapsible-body"><span>Lorem ipsum dolor sit amet.</span></div>
 +
          </li>
 +
            <li>
 +
          <div class="collapsible-header">
 +
              <div class="date-display">
 +
              <div class="date-display-cal">
 +
                <div class="date-display-month">
 +
                  Aug
 +
                </div>
 +
                <div class="date-display-day">
 +
                  8
 +
                </div>
 +
              </div>
 +
            </div>
 +
            <p>Note title</p></div>
 +
            <div class="collapsible-body"><span>Lorem ipsum dolor sit amet.</span></div>
 +
          </li>
 +
            <li>
 +
          <div class="collapsible-header">
 +
              <div class="date-display">
 +
              <div class="date-display-cal">
 +
                <div class="date-display-month">
 +
                  Aug
 +
                </div>
 +
                <div class="date-display-day">
 +
                  9
 +
                </div>
 +
              </div>
 +
            </div>
 +
            <p>Note title</p></div>
 +
            <div class="collapsible-body"><span>Lorem ipsum dolor sit amet.</span></div>
 +
          </li>
 +
            <li>
 +
          <div class="collapsible-header">
 +
              <div class="date-display">
 +
              <div class="date-display-cal">
 +
                <div class="date-display-month">
 +
                  Aug
 +
                </div>
 +
                <div class="date-display-day">
 +
                  10
 +
                </div>
 +
              </div>
 +
            </div>
 +
            <p>Note title</p></div>
 +
            <div class="collapsible-body"><span>Lorem ipsum dolor sit amet.</span></div>
 +
          </li>
 +
 
 +
        </ul>
 +
        <!-------------------------------------- END OF DAYS IN WEEK ---------------------------------------->
 +
 
 +
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 +
 
 +
        <!------------------------------------------- END OF WEEK --------------------------------------------->
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<!------------------------------------------- WEEK --------------------------------------------------->
 +
      <li>
 +
      <div class="collapsible-header">
 +
          <div class="date-display">
 +
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 +
                  Week
 +
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                <div class="date-display-day">
 +
                  33
 +
                </div>
 +
              </div>
 +
            </div>
 +
            <p>Note title</p></div>
 +
      <div class="collapsible-body"><span>
 +
 
 +
        <!----------------------------------------- DAYS IN WEEK ------------------------------------------->
 +
        <ul class="collapsible">
 +
          <li>
 +
            <div class="collapsible-header">
 +
              <div class="date-display">
 +
              <div class="date-display-cal">
 +
                <div class="date-display-month">
 +
                  Aug
 +
                </div>
 +
                <div class="date-display-day">
 +
                  13
 +
                </div>
 +
              </div>
 +
            </div>
 +
            <p>Note title</p></div>
 +
            <div class="collapsible-body"><span>Lorem ipsum dolor sit amet.</span></div>
 +
          </li>
 +
            <li>
 +
          <div class="collapsible-header">
 +
              <div class="date-display">
 +
              <div class="date-display-cal">
 +
                <div class="date-display-month">
 +
                  Aug
 +
                </div>
 +
                <div class="date-display-day">
 +
                  14
 +
                </div>
 +
              </div>
 +
            </div>
 +
            <p>Note title</p></div>
 +
            <div class="collapsible-body"><span>Lorem ipsum dolor sit amet.</span></div>
 +
          </li>
 +
            <li>
 +
          <div class="collapsible-header">
 +
              <div class="date-display">
 +
              <div class="date-display-cal">
 +
                <div class="date-display-month">
 +
                  Aug
 +
                </div>
 +
                <div class="date-display-day">
 +
                  15
 +
                </div>
 +
              </div>
 +
            </div>
 +
            <p>Note title</p></div>
 +
            <div class="collapsible-body"><span>Lorem ipsum dolor sit amet.</span></div>
 +
          </li>
 +
            <li>
 +
          <div class="collapsible-header">
 +
              <div class="date-display">
 +
              <div class="date-display-cal">
 +
                <div class="date-display-month">
 +
                  Aug
 +
                </div>
 +
                <div class="date-display-day">
 +
                  16
 +
                </div>
 +
              </div>
 +
            </div>
 +
            <p>Note title</p></div>
 +
            <div class="collapsible-body"><span>Lorem ipsum dolor sit amet.</span></div>
 +
          </li>
 +
            <li>
 +
          <div class="collapsible-header">
 +
              <div class="date-display">
 +
              <div class="date-display-cal">
 +
                <div class="date-display-month">
 +
                  Aug
 +
                </div>
 +
                <div class="date-display-day">
 +
                  17
 +
                </div>
 +
              </div>
 +
            </div>
 +
            <p>Note title</p></div>
 +
            <div class="collapsible-body"><span>Lorem ipsum dolor sit amet.</span></div>
 +
          </li>
 +
 
 +
        </ul>
 +
        <!-------------------------------------- END OF DAYS IN WEEK ---------------------------------------->
 +
 
 +
      </li>
 +
 
 +
        <!------------------------------------------- END OF WEEK --------------------------------------------->
 +
<!------------------------------------------- WEEK --------------------------------------------------->
 +
      <li>
 +
      <div class="collapsible-header">
 +
          <div class="date-display">
 +
              <div class="date-display-cal">
 +
                <div class="date-display-month">
 +
                  Week
 +
                </div>
 +
                <div class="date-display-day">
 +
                  34
 +
                </div>
 +
              </div>
 +
            </div>
 +
            <p>Note title</p></div>
 +
      <div class="collapsible-body"><span>
 +
 
 +
        <!----------------------------------------- DAYS IN WEEK ------------------------------------------->
 +
        <ul class="collapsible">
 +
          <li>
 +
            <div class="collapsible-header">
 +
              <div class="date-display">
 +
              <div class="date-display-cal">
 +
                <div class="date-display-month">
 +
                  Aug
 +
                </div>
 +
                <div class="date-display-day">
 +
                  20
 +
                </div>
 +
              </div>
 +
            </div>
 +
            <p>Note title</p></div>
 +
            <div class="collapsible-body"><span>Lorem ipsum dolor sit amet.</span></div>
 +
          </li>
 +
            <li>
 +
          <div class="collapsible-header">
 +
              <div class="date-display">
 +
              <div class="date-display-cal">
 +
                <div class="date-display-month">
 +
                  Aug
 +
                </div>
 +
                <div class="date-display-day">
 +
                  21
 +
                </div>
 +
              </div>
 +
            </div>
 +
            <p>Note title</p></div>
 +
            <div class="collapsible-body"><span>Lorem ipsum dolor sit amet.</span></div>
 +
          </li>
 +
            <li>
 +
          <div class="collapsible-header">
 +
              <div class="date-display">
 +
              <div class="date-display-cal">
 +
                <div class="date-display-month">
 +
                  Aug
 +
                </div>
 +
                <div class="date-display-day">
 +
                  22
 +
                </div>
 +
              </div>
 +
            </div>
 +
            <p>Note title</p></div>
 +
            <div class="collapsible-body"><span>Lorem ipsum dolor sit amet.</span></div>
 +
          </li>
 +
            <li>
 +
          <div class="collapsible-header">
 +
              <div class="date-display">
 +
              <div class="date-display-cal">
 +
                <div class="date-display-month">
 +
                  Aug
 +
                </div>
 +
                <div class="date-display-day">
 +
                  23
 +
                </div>
 +
              </div>
 +
            </div>
 +
            <p>Note title</p></div>
 +
            <div class="collapsible-body"><span>Lorem ipsum dolor sit amet.</span></div>
 +
          </li>
 +
            <li>
 +
          <div class="collapsible-header">
 +
              <div class="date-display">
 +
              <div class="date-display-cal">
 +
                <div class="date-display-month">
 +
                  Aug
 +
                </div>
 +
                <div class="date-display-day">
 +
                  24
 +
                </div>
 +
              </div>
 +
            </div>
 +
            <p>Note title</p></div>
 +
            <div class="collapsible-body"><span>Lorem ipsum dolor sit amet.</span></div>
 +
          </li>
 +
 
 +
        </ul>
 +
        <!-------------------------------------- END OF DAYS IN WEEK ---------------------------------------->
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Revision as of 10:12, 11 July 2018

Lab Journal


  • Week
    25

    NOTE TITLE

    • Jun
      18

      Note title

      Test.
    • Jun
      19

      Note title

      Lorem ipsum dolor sit amet.
    • Jun
      20

      Our first day in the laboratory!

      Goal: Incubate the Escherichia coli (E. coli) samples which carry pgRNA and pdCas9 on agar plates with antibiotics.

      Preparation of LA- medium
      LA- medium (1.5%) were made after the following recipe, and autoclaved for 20min at 121°C.
      • 1L Distilled water
      • 5g Yeast extract
      • 10g Tryptone
      • 5g NaCl
      • 15g Agar

      Agar plates with antibiotics
      Two different agar plates were made – one type contains ampicillin (AMP) while the other type contains chloramphenicol (CM), and were prepared after the following recipe:

      LA- medium with AMP:
      • 0.5L LA-medium
      • 0.5mL AMP (50mg/mL)
      LA-medium with CM:
      • 0.5L LA-medium
      • 0.5mL CM (35mg/mL)

      The LA-media with antibiotic were poured on petri dishes.

      Incubation of bacteria
      Two Escherichia coli (E. coli) samples which carry pgRNA and pdCas9 plasmids respectively, were ordered from Addgene. E.coli which carry the pgRNA plasmid were plated on agar plates with AMP, while E.coli which carry the pdCas9 plasmid were plated on two agar plates with CM, and incubated at 37℃.

      Results:
      The E.coli with pgRNA and pdCas9 formed colonies on the agar plates with AMP and CM
    • Jun
      21

      Inoculation of E.coli

      Goal: Inoculate a colony from each agar plate which were prepared from the previous day, in LB- medium with antibiotics.

      Procedure
      One colony of pgRNA- and pdCas9- bacteria grown overnight on agar plates were picked and inoculated in LB-media (25mL) with AMP (25μL) and CM (25μL), respectively. The cell cultures were incubated at 37℃ in a shaking incubator at 204rpm.
    • Jun
      22

      Isolation and verification of pgRNA and pdCas9

      Goal: Isolate and verify that the E.coli carry pgRNA and pdCas9.

      Plasmid isolation
      pgRNA and pdCas9 were isolated from the incubated bacteria prepared yesterday (June 21) by following the protocol of ZR Plasmid Miniprep Kit:
      1. 1mL of each cell culture (which either carry pgRNA or pdCas9) were transferred to eppendorf tube and centrifugated for 20s at 16000g
      2. The supernatant was discarded, while the pellet was resuspended in buffer
      3. Lysing buffer was added to the sample and carefully mixed in 2min
      4. Neutralizing buffer was added to the sample, and mixed until the colour of the solution became yellow
      5. The solution was centrifugated for 2min at 16000g
      6. The supernatant was collected and transferred to column in a collection tube, and centrifugated for 30s at 16000g
      7. The supernatant in the collection tube was discarded
      8. Endo-wash buffer was added to the column and centrifugated for 1min at 16000g
      9. Plasmid- wash buffer was added to the column and centrifugated for 1 min at 16000g
      10. The solution in the collection tube was discarded, while the column with plasmids was transferred to a new collection tube
      11. The plasmids in the column were eluted by adding 30μL distilled water, and centrifugated for 30s in 16000g

      Determine plasmid concentration and purity
      The concentration of plasmids and the purity of each sample were determined by using Nanodrop.

      Restriction digest and plasmid verification
      The presence of pgRNA and pdCas9 in the cell cultures were verified after following the restriction digest protocol and separation of the DNA fragments by gel electrophoresis.
  • Week
    26

    Note title

    • Jun
      25

      Note title

      Lorem ipsum dolor sit amet.
    • Jun
      26

      Note title

      Lorem ipsum dolor sit amet.
    • Jun
      27

      Note title

      Lorem ipsum dolor sit amet.
    • Jun
      28

      Note title

      Lorem ipsum dolor sit amet.
    • Jun
      29

      Note title

      Lorem ipsum dolor sit amet.
  • Week
    27

    Note title

    • Jul
      1

      Note title

    • Jul
      2

      InterLabs Study

      Calibration 1 and 2 for the InterLabs Study.
    • Jul
      3

      Note title

      Lorem ipsum dolor sit amet.
    • Jul
      4

      Note title

      Lorem ipsum dolor sit amet.
    • Jul
      5

      Note title

      Lorem ipsum dolor sit amet.
  • Week
    28

    Note title

    • Jul
      9

      Note title

      Lorem ipsum dolor sit amet.
    • Jul
      10

      Note title

      Lorem ipsum dolor sit amet.
    • Jul
      11

      Note title

      Lorem ipsum dolor sit amet.
    • Jul
      12

      Note title

      Lorem ipsum dolor sit amet.
    • Jul
      13

      Note title

      Lorem ipsum dolor sit amet.
  • Week
    29

    Note title

    • Jul
      16

      Note title

      Lorem ipsum dolor sit amet.
    • Jul
      17

      Note title

      Lorem ipsum dolor sit amet.
    • Jul
      18

      Note title

      Lorem ipsum dolor sit amet.
    • Jul
      19

      Note title

      Lorem ipsum dolor sit amet.
    • Jul
      20

      Note title

      Lorem ipsum dolor sit amet.
  • Week
    30

    Note title

    • Jul
      23

      Note title

      Lorem ipsum dolor sit amet.
    • Jul
      24

      Note title

      Lorem ipsum dolor sit amet.
    • Jul
      25

      Note title

      Lorem ipsum dolor sit amet.
    • Jul
      26

      Note title

      Lorem ipsum dolor sit amet.
    • Jul
      27

      Note title

      Lorem ipsum dolor sit amet.
  • Week
    31

    Note title

    • Jul
      30

      Note title

      Lorem ipsum dolor sit amet.
    • Jul
      31

      Note title

      Lorem ipsum dolor sit amet.
    • Aug
      1

      Note title

      Lorem ipsum dolor sit amet.
    • Aug
      2

      Note title

      Lorem ipsum dolor sit amet.
    • Aug
      3

      Note title

      Lorem ipsum dolor sit amet.
  • Week
    32

    Note title

    • Aug
      6

      Note title

      Lorem ipsum dolor sit amet.
    • Aug
      7

      Note title

      Lorem ipsum dolor sit amet.
    • Aug
      8

      Note title

      Lorem ipsum dolor sit amet.
    • Aug
      9

      Note title

      Lorem ipsum dolor sit amet.
    • Aug
      10

      Note title

      Lorem ipsum dolor sit amet.
  • Week
    33

    Note title

    • Aug
      13

      Note title

      Lorem ipsum dolor sit amet.
    • Aug
      14

      Note title

      Lorem ipsum dolor sit amet.
    • Aug
      15

      Note title

      Lorem ipsum dolor sit amet.
    • Aug
      16

      Note title

      Lorem ipsum dolor sit amet.
    • Aug
      17

      Note title

      Lorem ipsum dolor sit amet.
  • Week
    34

    Note title

    • Aug
      20

      Note title

      Lorem ipsum dolor sit amet.
    • Aug
      21

      Note title

      Lorem ipsum dolor sit amet.
    • Aug
      22

      Note title

      Lorem ipsum dolor sit amet.
    • Aug
      23

      Note title

      Lorem ipsum dolor sit amet.
    • Aug
      24

      Note title

      Lorem ipsum dolor sit amet.